Protobothrops mucrosquamatus is the endangered snake that is distributed in southwestern China and other adjacent countries of Asia. We determined the complete mitochondrial genome of P. mucrosquamatus. The circle genome with the total length of 17,233 bp contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 control regions. Overall base composition of the complete mtDNA was 32.98% A, 25.17% T, 29.19% C and 12.67% G. All the genes in P. mucrosquamatus were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes that were encoded on the L-strand.